Questions tagged [proteins]

Questions relating to proteins, the chains of amino acids that form three-dimensional structures carrying important functions of life. Protein sequence, structure, similarity, domains, etc.

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Why ace2 is not included in SARS-COV-2 PPIN map?

I'm doing my master's thesis on drug repositioning for sars-cov-2 using AI more specificaly network medicine, I found only one PPIN map from Gordon et al. but it doesn't include the ace2 protein which ...
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2answers
1k views

How to select a cutoff for interaction confidence in STRINGdb?

I have a list of 100 genes that are called as hits in a genetic screening. I want to have a network of the interactions between the proteins of these 100 genes. I am using both STRINGdb web and its R ...
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2answers
267 views

Web scraping in R

I have ~130 gene names of different human proteins. I'm looking for a convenient and systematic way to locate each gene's location in the genome, extract its CDS sequence and find whether there are ...
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1answer
42 views

Automating download of results of Drug and Drug Target Mapping

The drug and drug target mapping tool shows the top 3 PDB IDs for each drug based on the drug target sequence similarity search and ligand id search. Is there a way to get all the PDB ids of the drug-...
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1answer
61 views

Is there a modern alignment tool tailored for transmembrane regions?

I am looking for a project or tool that allows programmatic pairwise alignments of proteins but that takes care with transmembrane regions of proteins. TM regions are traditionally too information ...
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69 views

Minimizing particle-flow grid mapping time of a protein surface using spherical-coordinates and differentiation encoding [closed]

This is an interesting problem - I was wondering if anyone has a creative solution. So I have a vector of vertices representing atoms in a protein, as well as 6 variables containing the absolute ...
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0answers
29 views

Convert .smp from CDD into HMM file

Is there a method or tool to convert a .smp file from CDD (Protein Domain File) into a HMM file? I downloaded the CDD files from the FTP site and am more familiar with domain searching with the HMMer ...
2
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1answer
57 views

How do you calculate the top L/5 score?

I am currently investigating how to predict protein structure and contact map predictions. There, I see things like top L/5 and top L/2 scores as a way to evaluate the contact map. What formulas do ...
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1answer
25 views

Holistic enzyme activity determination with computation [closed]

I'm currently working on a program which will determine the activity difference between an original enzyme and a variant with just 1 or 2 variants. Of course, I'm not talking about the "kinetic ...
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1answer
60 views

amino acids substitution probability [closed]

I'm looking for the probabilities of amino acid substitutions in protein sequences. A matrix of probabilities for every combination of amino acids (something like BLOSUM or PAM matrices but more ...
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1answer
63 views

Translating a genome sequence into possible frames

I have a sequence below from MYC gene about which I need to translate the sequence in all possible frames AND identify (for each frame) which codons are actually used in MYC ...
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1answer
24 views

How to get 2d/3d structural coordinates from a PDB file?

Is there a way we can get 2d/3d structural coordinates like in (x/y/z) manner from a pdb file. I have looked a believe that the coordinates are in below line: ...
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1answer
44 views

Do proteins move inside the cell? [closed]

Do proteins move inside the cell and how fast do they move or move? Please support your answer with articles or books.
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1answer
27 views

Extract features from fasta sequences and train the classifier

I am new to the bioinformatics field. I have positive and negative protein sequences for acetylation PTM. Now, I want to train a classifier, say SVM. What will be the next step? How can I convert ...
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3answers
122 views

Database for proteome-wide predictions of protein structures

Accuracies of protein structure predictors have improved quite a lot in recent years. Algorithms such as Rosetta have gotten robust enough to predict structures of large number of proteins. However, I ...
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13 views

phosphosite nomenclature and conversion (phosphoproteomics)

I have a dataset containing the following kind of phosphorylation sites nomenclature: ...
2
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1answer
140 views

MSA (protein) with biopython or something else?

I am very new to bioinformatics (and python in general), but I would like to use python to more efficiently analyse enzymes both in terms of structure and functio, using Jupiter notebook. I would like ...
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1answer
53 views

Align the HIV-1 Gag protein with the Gag protein of Visna virus

Align the HIV-1 Gag protein with the Gag protein of Visna virus Background Visna virus is a lentivirus causing encephalitis in sheep The problem is align the follow two protein Gag of viruses HIV-1 (...
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2answers
107 views

Why GAG protein HIV-1 (virus) is in Staphylococcus sp. SS21 and in Klebsiella quasipneumoniae (Bacteria)?

I am one ignorant... Why GAG protein HIV-1 (virus) is in Staphylococcus sp. SS21 and in Klebsiella quasipneumoniae (Bacteria)? These are the links in GenBank: ...
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25 views

Java Protein Comparison Visualisation

I have project where I am required to build a visual analytics tool into an existing Java project to visually compare and analyse protein sequences from SwissProt, GenBank, EMBL etc. (downloaded from ...
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2answers
32 views

Functional Annotation vs Functional Enrichment--which one should I use for Network Analysis?

I am currently working on a network pharmacology project where I am supposed to find out the possible diseases our drug might have an effect on. I am not a bioinformatics student, so my knowledge in ...
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2answers
67 views

How can I convert Protein ID to PDB ID?

I have a list of Protein ID such as Q9S9U6, A2XLL2, Q06402. What name is this ID? UniProtKB ID? And how can I get PDB ID from this list? Is its PDB ID only one? I'm using Python. Get a list of PDB ids ...
2
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1answer
103 views

Human Herpes Virus, fusion motif in protein vs. SARS-CoV-2?

Is it possible that the fusion with cell propriety of Human Herpes virus, I see X14112.1 in GenBank is due to protein UL36 (tegument of virus) starting in linear position 2685 ??? ...
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1answer
78 views

What unit is the length of a protein measured in?

Sorry if this question is obvious - I'm not familiar with proteomics so I'm not sure of the standard units. In this paper, it talks about using the length of a protein to calculate the NSAF value. ...
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1answer
101 views

What origins for virus HIV1?

What origins for virus HIV1? This is the alignment of a small part of the POL protein of the HIV1 virus GenBank KU749412.1, with the POL protein of the Visna virus GenBank L06906.1 ...
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33 views

How can I get properties from each one letter amino acid?

Im using python and wish to get properties from each one letter amino acid? I mean M(Met) => Density:1.340, MW:149.21... The RDkit methods atom.GetSymbol(), atom.GetDegree() permit this and I am ...
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1answer
83 views

Identification of starting point for the synthesis of a protein

identify where is the starting point for the synthesis of a protein in the DNA For indentify a starting point in RNA or DNA my function search all ATG or M in the sequece and report the linear ...
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3answers
1k views

How to translate amino acid sequences to Nucleotide sequences

I want to convert a list of fasta ( protein sequences) in a .text file into corresponding nucleotide sequences. A Google search gives me result of DNA to protein conversion but not vice versa. Also, I ...
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0answers
6 views

Mutated residue number shown wrong in foldX yasara

I am trying to mutate phenylalanine 274 position in Uracil DNA glycosylase with alanine. The pDB file has the protein starting from 82nd residue. After the repair the console shows FA161A. The residue ...
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0answers
76 views

Can VMD change its cartoon representation for secondary structure according to trajectories?

I am using VMD to visualise the secondary structure of protein here. The trajectories are from my Gromacs simulation. Firstly I use ...
3
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2answers
162 views

How to find/build the evolutionary history of a protein from its sequence?

I'd like to build the evolutionary history of a protein, given its sequence. Namely, given a FASTA entry how can I build an evolutionary tree? Here is the 5wxy protein as an example: ...
3
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1answer
41 views

Folded Protein Chunk Dimensional Classification?

Are there known dimensional measurements for the classification of folded proteins given a starting chunk/domain as defined by something like the clustering functionality of MSM Builder? Examples of ...
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1answer
54 views

Mining documents for nucleotide and peptide sequences

The text mining literature has an emphasis on identifying and normalizing gene names, mutations, pathways, concepts, and so on. I haven't been able to find much, however, on methods for extracting ...
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40 views

Python/Biopython - Replace amino acid residue on MSA with “z” from a list of unaligned positions

I'm trying to programmatically replace a set of amino acid residues on an MSA with a "Z" from a list of unaligned positions. Any ideas on how I could do this? Input: a list of unaligned ...
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36 views

Please help me with my command!

I am looking for a command to count the total number of unique proteins in a file. For instance I wrote a command to BLAST XYZ proteins as query against the DLY proteins as a database to determine the ...
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1answer
37 views

How many entries in PDB have SS bonds?

Is there a way to figure out what percentage of entries in PDB have SS bonds? In addition, what other types of bonds in PDB may be worth looking into (not H bonds)?
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0answers
24 views

Error while splitting PDBQT file

I am trying to split to a pdbqt file containing 178 compounds into individual pdbqt files. I have been using the Autodock Vina_split.exe file to split the multiple entry file however I keep running ...
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2answers
44 views

What programs account for structural alignment of different parts of distant homologs which have significant structural differences?

If there is a need to perform structural alignment of different parts of distant homologs, which program one should use? Since distant homologs often have significant structural changes, meaning the ...
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1answer
43 views

Finding discriminating positions for a sequence alignment column

I don't have any theoretical background in biology, so forgive me if my question is a bit.. well..dumb. I'm trying to use a Monte Carlo approach to find the discriminating position of a given sequence ...
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1answer
211 views

Is there any tool for fuzzy sequence matching?

Note: this question was also asked on biostars are you aware of any tool that is able to perform error-tolerant pattern-matching search on protein FASTA files? For example, I want to know, which ...
2
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1answer
50 views

PDB residue numbering

The residue numbering in PDB (in my understanding) coincides with UniProtKB align. However, this might not be consistent with that in PDB fasta file. To complicate it further, UniProtKB align can be a ...
2
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1answer
57 views

Principle of TMT Tags in Multiplex Proteomics

I am new to proteomics research and analyzing mass-spec data. I am trying to learn more about the theory/principle of TMT tagging (a type of isobaric labeling) coupled with LC-MS/MS spectrometry. I ...
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1answer
33 views

B-factor analysis in nanobodies

I am doing my research on nanobodies. Currently, I am trying to do a comparison study of the flexibility of CDR loops using B-factor values. I would like to know if there is any statistical analysis ...
1
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1answer
67 views

Modifying protein_scale in ProteinAnalysis in SeqUtil in Biopython?

Is there a way to give weight arguments to each of the residues when using protein_scale in the ProteinAnalysis module of Bio.SeqUtils.ProtParam? I thought this would be done with the window and edge ...
0
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1answer
74 views

Seurat DE t.test

I am new to the Seurat package and was looking at the tutorials on the Seurat website and am just curious to know if there is any way to perform a t.test for the expression of a specific gene between ...
3
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1answer
1k views

Searching for start and stop codons for protein sequencing of contigs

I need to convert contigs into their respective protein sequences given a reference genome (i.e. I need to take a substring, whose position is already known on the string, and I need to locate the ...
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1answer
29 views

Calculating Isoelectric point from a multifasta file

I need to calculate Isoelectric point from a multifasta file, is there any python code or web tool that allows me to do that?
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1answer
48 views

Methods to predict one connected structure from two known separate structures

Currently, I am facing such a question: how to predict one connected protein structures from two separate known structures? It should be different from the protein-protein docking method, which is ...
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1answer
122 views

How do I convert an Excel file (.xlsx) to an .smi file format?

How do I convert an Excel file(.xlsx) to .smi file format? The original file I have is an excel file containing over 27,000 ligands. I am going to using the Padel Descriptor software to calculate the ...
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1answer
27 views

Is it possible to predict protein-ligand binding kinetics using machine learning? [closed]

I would like to work on a project that involves the prediction of protein-ligand binding kinetics. What might be the feature that is relevant for the prediction?